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Manganese in PDB 2ioc: The Crystal Structure of TREX1 Explains the 3' Nucleotide Specificity and Reveals A Polyproline II Helix For Protein Partenring

Enzymatic activity of The Crystal Structure of TREX1 Explains the 3' Nucleotide Specificity and Reveals A Polyproline II Helix For Protein Partenring

All present enzymatic activity of The Crystal Structure of TREX1 Explains the 3' Nucleotide Specificity and Reveals A Polyproline II Helix For Protein Partenring:
3.1.11.2;

Protein crystallography data

The structure of The Crystal Structure of TREX1 Explains the 3' Nucleotide Specificity and Reveals A Polyproline II Helix For Protein Partenring, PDB code: 2ioc was solved by U.De Silva, T.Hollis, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 25.00 / 2.10
Space group H 3
Cell size a, b, c (Å), α, β, γ (°) 119.700, 119.700, 83.300, 90.00, 90.00, 120.00
R / Rfree (%) 19.8 / 24.3

Manganese Binding Sites:

The binding sites of Manganese atom in the The Crystal Structure of TREX1 Explains the 3' Nucleotide Specificity and Reveals A Polyproline II Helix For Protein Partenring (pdb code 2ioc). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 4 binding sites of Manganese where determined in the The Crystal Structure of TREX1 Explains the 3' Nucleotide Specificity and Reveals A Polyproline II Helix For Protein Partenring, PDB code: 2ioc:
Jump to Manganese binding site number: 1; 2; 3; 4;

Manganese binding site 1 out of 4 in 2ioc

Go back to Manganese Binding Sites List in 2ioc
Manganese binding site 1 out of 4 in the The Crystal Structure of TREX1 Explains the 3' Nucleotide Specificity and Reveals A Polyproline II Helix For Protein Partenring


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of The Crystal Structure of TREX1 Explains the 3' Nucleotide Specificity and Reveals A Polyproline II Helix For Protein Partenring within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn401

b:16.4
occ:1.00
 OD2 B:ASP200 2.0 11.8 1.0
OE1 B:GLU20 2.1 17.7 1.0
OD2 B:ASP18 2.2 10.8 1.0
O1P B:D5M303 2.3 13.7 1.0
O3P B:D5M303 2.4 17.1 1.0
P B:D5M303 2.9 20.5 1.0
CD B:GLU20 2.9 14.4 1.0
OE2 B:GLU20 3.1 15.9 1.0
CG B:ASP200 3.1 13.4 1.0
CG B:ASP18 3.2 11.4 1.0
OD1 B:ASP18 3.4 8.6 1.0
CB B:ASP200 3.6 12.5 1.0
MN B:MN402 3.6 11.4 1.0
O2P B:D5M303 3.7 18.9 1.0
O B:HOH516 3.8 14.6 1.0
CA B:HIS195 3.9 22.3 1.0
O5' B:D5M303 3.9 16.7 1.0
C B:HIS195 4.2 21.3 1.0
N B:THR196 4.2 19.3 1.0
O B:LEU19 4.2 13.3 1.0
OD1 B:ASP200 4.2 12.3 1.0
O B:THR196 4.3 12.8 1.0
C5' B:D5M303 4.3 15.5 1.0
CG B:GLU20 4.3 14.9 1.0
N B:HIS195 4.4 22.8 1.0
C B:THR196 4.4 16.5 1.0
O B:HOH500 4.5 14.7 1.0
CB B:ASP18 4.6 11.2 1.0
O B:HOH474 4.6 12.5 1.0
N B:ALA197 4.7 15.2 1.0
CA B:ALA197 4.8 16.5 1.0
O B:HOH528 4.9 19.8 1.0
O B:HIS195 4.9 20.7 1.0
C B:LEU19 4.9 14.6 1.0
O B:HOH508 4.9 15.1 1.0
CA B:THR196 5.0 17.4 1.0
ND1 B:HIS195 5.0 26.9 1.0

Manganese binding site 2 out of 4 in 2ioc

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Manganese binding site 2 out of 4 in the The Crystal Structure of TREX1 Explains the 3' Nucleotide Specificity and Reveals A Polyproline II Helix For Protein Partenring


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of The Crystal Structure of TREX1 Explains the 3' Nucleotide Specificity and Reveals A Polyproline II Helix For Protein Partenring within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn402

b:11.4
occ:1.00
 O1P B:D5M303 2.0 13.7 1.0
O B:HOH516 2.0 14.6 1.0
OD1 B:ASP18 2.1 8.6 1.0
O B:HOH473 2.1 13.6 1.0
O B:HOH474 2.2 12.5 1.0
O B:HOH508 2.3 15.1 1.0
CG B:ASP18 3.2 11.4 1.0
P B:D5M303 3.3 20.5 1.0
O2P B:D5M303 3.6 18.9 1.0
MN B:MN401 3.6 16.4 1.0
OD2 B:ASP18 3.6 10.8 1.0
O B:HOH519 3.9 5.1 1.0
OD2 B:ASP130 4.0 14.8 1.0
C5' B:D5M303 4.0 15.5 1.0
OD1 B:ASP130 4.1 15.8 1.0
O5' B:D5M303 4.1 16.7 1.0
O B:LEU19 4.1 13.3 1.0
O B:HOH500 4.2 14.7 1.0
O B:HOH506 4.3 16.4 1.0
O B:HIS124 4.3 12.2 1.0
O B:HOH501 4.4 19.8 1.0
O3P B:D5M303 4.4 17.1 1.0
CB B:ASP18 4.4 11.2 1.0
CG B:ASP130 4.5 14.0 1.0
N B:LEU19 4.6 13.5 1.0
CA B:ASP18 4.7 12.0 1.0
OD2 B:ASP200 4.9 11.8 1.0

Manganese binding site 3 out of 4 in 2ioc

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Manganese binding site 3 out of 4 in the The Crystal Structure of TREX1 Explains the 3' Nucleotide Specificity and Reveals A Polyproline II Helix For Protein Partenring


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of The Crystal Structure of TREX1 Explains the 3' Nucleotide Specificity and Reveals A Polyproline II Helix For Protein Partenring within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn403

b:18.7
occ:1.00
 OD2 A:ASP200 2.0 13.3 1.0
OE1 A:GLU20 2.0 15.1 1.0
O3P A:D5M302 2.0 20.6 1.0
OD2 A:ASP18 2.3 19.1 1.0
CD A:GLU20 2.8 15.6 1.0
CG A:ASP200 3.1 13.4 1.0
OE2 A:GLU20 3.1 18.9 1.0
CG A:ASP18 3.2 17.2 1.0
P A:D5M302 3.2 26.4 1.0
O2P A:D5M302 3.3 25.7 1.0
OD1 A:ASP18 3.3 17.1 1.0
O A:HOH467 3.5 34.9 1.0
CB A:ASP200 3.6 13.3 1.0
MN A:MN404 3.7 19.2 1.0
O A:HOH466 3.9 13.8 1.0
O5' A:D5M302 4.0 22.6 1.0
CA A:HIS195 4.1 26.4 1.0
O A:LEU19 4.1 14.6 1.0
OD1 A:ASP200 4.1 12.3 1.0
CG A:GLU20 4.2 16.0 1.0
C A:HIS195 4.2 24.0 1.0
O A:THR196 4.2 17.5 1.0
N A:THR196 4.3 22.0 1.0
C5' A:D5M302 4.4 23.6 1.0
O1P A:D5M302 4.4 28.7 1.0
C A:THR196 4.4 17.9 1.0
O A:HOH468 4.5 19.2 1.0
N A:HIS195 4.6 27.5 1.0
O A:HOH448 4.6 23.4 1.0
CB A:ASP18 4.6 16.0 1.0
N A:ALA197 4.7 15.6 1.0
CA A:ALA197 4.8 13.0 1.0
O A:HIS195 4.8 24.8 1.0
C A:LEU19 4.8 15.8 1.0
ND1 A:HIS195 4.9 28.9 1.0

Manganese binding site 4 out of 4 in 2ioc

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Manganese binding site 4 out of 4 in the The Crystal Structure of TREX1 Explains the 3' Nucleotide Specificity and Reveals A Polyproline II Helix For Protein Partenring


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of The Crystal Structure of TREX1 Explains the 3' Nucleotide Specificity and Reveals A Polyproline II Helix For Protein Partenring within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn404

b:19.2
occ:1.00
 O A:HOH466 2.0 13.8 1.0
O A:HOH510 2.1 18.2 1.0
OD1 A:ASP18 2.2 17.1 1.0
O A:HOH468 2.2 19.2 1.0
O3P A:D5M302 2.3 20.6 1.0
O1P A:D5M302 2.8 28.7 1.0
P A:D5M302 3.1 26.4 1.0
CG A:ASP18 3.3 17.2 1.0
MN A:MN403 3.7 18.7 1.0
O2P A:D5M302 3.9 25.7 1.0
OD2 A:ASP18 3.9 19.1 1.0
O A:HOH448 3.9 23.4 1.0
O A:HOH497 4.0 9.9 1.0
OD2 A:ASP130 4.0 18.3 1.0
C5' A:D5M302 4.1 23.6 1.0
O5' A:D5M302 4.1 22.6 1.0
O A:HOH506 4.2 15.1 1.0
O A:HIS124 4.2 15.1 1.0
O A:LEU19 4.2 14.6 1.0
OD1 A:ASP130 4.2 19.1 1.0
O A:HOH515 4.5 23.5 1.0
CB A:ASP18 4.5 16.0 1.0
CG A:ASP130 4.6 19.1 1.0
N A:LEU19 4.7 14.6 1.0
OD2 A:ASP200 4.8 13.3 1.0
CA A:ASP18 4.8 14.8 1.0

Reference:

U.De Silva, S.Choudhury, S.L.Bailey, S.Harvey, F.W.Perrino, T.Hollis. The Crystal Structure of TREX1 Explains the 3' Nucleotide Specificity and Reveals A Polyproline II Helix For Protein Partnering. J.Biol.Chem. V. 282 10537 2007.
ISSN: ISSN 0021-9258
PubMed: 17293595
DOI: 10.1074/JBC.M700039200
Page generated: Sat Oct 5 14:29:53 2024

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